Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.20.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00197	0.858
27DAP/17DAP	1.18205	0.845
39DAP/27DAP	1.29378	0.579
41DAP/39DAP	0.92963	0.681
42DAP/41DAP	0.78316	0.774
43DAP/42DAP	1.31956	0.682
47DAP/43DAP	1.08294	0.95
52DAP/47DAP	1.24449	0.601
57DAP/52DAP	1.00884	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17583	0.059
17DAP/reference	0.93752	0.028
27DAP/reference	0.78936	0.095
39DAP/reference	0.83845	0.118
41DAP/reference	0.83749	0.008
42DAP/reference	1.06268	0.68
43DAP/reference	0.68828	0.5
47DAP/reference	1.04319	0.612
52DAP/reference	1.1232	0.951
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99533	0.826
27DAP/17DAP	0.9839	0.919
39DAP/27DAP	0.96366	0.759
41DAP/39DAP	1.3392	0.656
42DAP/41DAP	0.95391	0.67
43DAP/42DAP	0.7565	0.024
47DAP/43DAP	0.998	1
52DAP/47DAP	0.95276	0.729
57DAP/52DAP	1.12147	0.35
57DAP/7DAP	0.64583	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48569	0.03
17DAP/reference	1.10529	0.328
27DAP/reference	1.18888	0.035
39DAP/reference	1.25811	0.005
41DAP/reference	1.23341	0.012
42DAP/reference	1.21249	0.046
43DAP/reference	1.12854	0.045
47DAP/reference	1.25333	0.029
52DAP/reference	1.31652	0.021
57DAP/reference	1.36136	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08929	0.507
17DAP/reference	1.16854	0.216
27DAP/reference	1.2377	0.203
39DAP/reference	1.10376	0.366
41DAP/reference	1.17379	0.109
42DAP/reference	1.07347	0.309
43DAP/reference	0.96792	0.552
47DAP/reference	1.35123	0.01
52DAP/reference	0.93757	0.239
57DAP/reference	0.93478	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23606	0.042
17DAP/reference	1.02998	0.728
27DAP/reference	1.07073	0.149
39DAP/reference	1.15528	0.029
41DAP/reference	1.08721	0.058
42DAP/reference	1.13804	0.158
43DAP/reference	1.21344	0.038
47DAP/reference	1.04757	0.63
52DAP/reference	1.56594	0.046
57DAP/reference	1.14517	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0956	0.966
26DAP/20DAP	1.53813	0.127
34DAP/26DAP	1.15074	1
51DAP/34DAP	0.87191	0.333
52DAP/51DAP	0.80184	1
53DAP/52DAP	1.02185	0.91
55DAP/53DAP	0.85064	0.252
57DAP/55DAP	1.03986	0.927
62DAP/57DAP	1.18549	0.767
68DAP/62DAP	1.28251	0.507
68DAP/14DAP	1.20591	0.915

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.59697	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.91405	0.491
Mature Green Tomato/Ripe Tomato	1.13312	0.267
Immature Eggplant/Mature Eggplant	1.20632	0.052
Ripe Pepper/Ripe Tomato	1.37993	1
Mature Eggplant/Ripe Tomato	1.5899	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95049	0.613
1-1-2/M82	1.09124	0.977
12-2/M82	1.0377	1
12-4/M82	1.06481	1
1-3/M82	1.03757	1
2-1-1/M82	1.01255	1
2-1/M82	0.98025
2-6/M82	0.96825	1
3-2/M82	1.00733	1
4-1-1/M82	1.0914	1
4-1/M82	1.4798	0.512
4-3-2/M82	1.10449	1
4-3/M82	1.21927	1
5-3/M82	1.12214	0.572
6-2/M82	0.91629	0.444
6-3/M82	1.01105	1
7-1/M82	1.02608	1
7-2/M82	1.07187	0.324
9-3-2/M82	1.18977	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.29397
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.69817
IL12-4/WTpooled	1.54829	0.532
IL1-4/WTpooled	0.77858
WT/WTpooled	0.8675	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.16506	0.167

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96198	0.839
DC3000/delta hrp 6h	1.00255	0.95
DC3000/delta hrp 12h	0.8956	1
DC3000/delta hrp 24h	1.16262	0.308

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.25203	0.183
DC3000 delta B/DC3000 delta AB	1.06383	0.453

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.74869	1
Exp 36h	1.29639	0.693
Exp 60h	1.14502	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.00765	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.10682	0.736
Var 12h NI row2-row1	1.14575	0.649
Var 36h I row2-row1	1.17652	0.309
Var 36h NI row2-row1	0.72936	0.225
Var 60h I row2-row1	0.88837	0.832
Var 60h NI row2-row1	0.85393	0.292
Time course 0hI-0hNI	0.83971	0.096
Time course 12hI-12hNI	1.04179	0.687
Time course 36hI-36hNI	1.33117	0.114
Time course 60hI-60hNI	1.38259	0.011

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.01973	0.921
transgenic ySAMdc/azygous control (breaker)	1.54892	0.248
transgenic ySAMdc/azygous control (red)	1.29802	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02865	0.495

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.69115	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.91852	1
Manapal/WT (break)	1.29038	0.381
Manapal/WT (red)	1.17315	0.222